A Reagan administration committee is trying to decide how much to charge business to launch manufacturing experiments into space, and the fortunes of two emerging industries are riding on the outcome.

At present, companies developing manufacturing processes for space pay nothing to launch experiments on the Space Shuttle. However, as soon as commercial technologies are viable -- within the next few years for some companies -- businesses will pay $34 million, or one-third, of the $100 million it is expected to cost for each shuttle mission, a NASA spokesman said.

In 1988, a new pricing structure will go into effect, under which the user will pay two-thirds of the cost. By the early 1990s, the subsidy will be eliminated. But the question administration officials are trying to resolve is what it actually costs to send a business payload into orbit.

Meanwhile, NASA also is turning over to the private sector old Atlas Centaur and Delta rockets for use in launching communications satellites. U.S. companies will handle those missions in competition with Arianespace, a European satellite-launching consortium.

Marketing rights to the Delta rocket have been taken over by Transpace Carriers Inc., and rights to the Atlas Centaur, by General Dynamics Corp. The rockets are expected to begin flying in 1986 and 1987.

According to Jennifer Dorn, director of the Department of Transportation's office of commercial space transportation, the administration's aim is "to avoid broad and sweeping subsidies of space transportation. . . . If we fail to go for full cost recovery, we will fail to capitalize on a private-sector resource."

But an official of McDonnell Douglas Astronautics Co. said, "If the private sector thinks the government is not going to be sensitive to pricing, companies will just walk away from manufacturing in space -- it's a shame, it's a vast industry."

Biotechnological and industrial-materials processing, remote sensing, advanced communications and other commercial space projects that depend on the shuttle and cannot be launched via the old rockets could be affected by new pricing policies, manufacturers say.

The McDonnell Douglas official, who asked not to be named, said his company has invested $150 million over the last seven years in a cell- and protein-separation process (electrophoresis) to be used in space. The potentially billion-dollar electrophoresis industry is expected to lead to new pharmaceutical products such as anticoagulant medicine.

Some government officials believe the companies should pay the actual cost of a shuttle launch because they don't want to put commercial rocket launchers at a disadvantage.

Others say eliminating the subsidy to protect the rocket-launching firms could backfire and send customers of the shuttle, as well as of the rockets, to Arianespace.

Officials say Arianespace consistently will undercut U.S. pricing for launch services because of European government subsidies.

The Cabinet Council on Commerce and Trade -- consisting of the secretaries of Transportation, Defense, Commerce, as well as the head of NASA and other government agencies -- is expected to recommend new prices and an overall space commercialization plan to President Reagan within a few months, sources said.

(The military also is concerned that it might lose out if the shuttle becomes too popular with commercial users. It is now the biggest customer for the shuttle, and another interagency group representing security interests has been formed to debate that issue.)

Some administration officials are arguing that the launch costs actually will be much higher than NASA calculates, and that manufacturers will have to pay more.

At the same time, business officials believe the price of the shuttle should be held to a minimum to nurture the new industry.

European countries are considering developing their own manufacturing industry in space and could win the race with the United States if shuttle prices become prohibitive, said Bruce Ferguson, vice president of finance for Orbital Sciences Corp., a manufacturer of upper-stage launchers used with the shuttle.